I wouldn't let it keep me from making beer. It would probably be better to have the cover, but I don't imagine it would matter much. The airlock will still be sealed when CO2 isn't being pushed out. The only potential problem I can see is that every time it bubbles there will be a path for oxygen to get into the carboy, since the cap isn't holding it submerged. You could probably solve that problem with a strategically arranged rubber band. But some brewers don't even use an airlock until after high kräusen, simply covering the opening with foil.